Open access peer-reviewed chapter
Abstract
Infection with the Dengue virus (DENV) has become a global threat, affecting approximately 100 nations. There is not a recognized antiviral treatment for dengue at the moment. Therefore, it is crucial to create therapeutic approaches to treat this fatal condition. A critical and successful method of silencing genes, RNA interference breaks down targeted RNA according to its sequence. Over the past ten years, a number of studies have been carried out to determine how well siRNA works to prevent dengue virus replication. CRISPR (clustered regularly interspaced short palindromic repeats) is becoming one of the most effective and widely used tools for RNA and DNA manipulation in numerous organisms. In our review, we describe and discuss the use of these technologies to comprehend and treat DENV-related infections.
Keywords
- dengue
- CRISPR
- RNAi
- genetic engineering
- siRNA
1. Introduction
Dengue is the most dangerous virus spread by mosquitoes, and any of the four DENV serotypes (DENV-1 to DENV-4) can cause it. A DENV infection can cause a broad spectrum of clinical symptoms, ranging from a mild flu-like condition known as dengue fever (DF) to the potentially fatal dengue shock syndrome (DSS) [1].
Approximately half of the global population is at risk for Dengue fever, and the mosquito-borne virus is the leading cause of death in certain Latin American and Asian nations. Nevertheless, despite the rapid increase in cases and decades of drug development efforts, there is no specific treatment and only one vaccine with a limited application [2].
Symptoms of DF include fever, nausea, vomiting, rash, and aches and pains; however, in DSS, severe hemorrhage and shock can develop, and if left untreated, the fatality rate can reach 20%. Previously, the World Health Organization (WHO) classified dengue disease states as undifferentiated fever, dengue fever, and dengue hemorrhagic fever (DHF) [3].
The categorization of DHF was revised into four levels of severity, with grades III and IV being classified as DSS. However, in 2009, the WHO updated its case categorization method, discontinuing the previous categories of probable Dengue, Dengue with unexpected symptoms, Dengue with warning symptoms, and severe Dengue. Currently, the focus is on understanding DENV’s biology, epidemiology, and transmission characteristics, including circulating serotypes and genotypes, DENV-specific immune responses, illness etiology, improved diagnostic tools, therapies, and vaccine development [2, 3].
There is no antiviral treatment for dengue fever, and the only approved vaccine, Dengvaxia from Sanofi, can be dangerous. Dengvaxia can reduce the severity of Dengue fever in previously infected individuals. However, Dengvaxia may increase the risk of severe Dengue in uninfected individuals [4].
Experts say that the development of vaccines and antivirals has been slowed down by poorly coordinated clinical trials, problems with animal models and lab tests, and a complicated and constantly changing virus. Experts say that manufacturers could make progress on this disease if they simplified the endpoints for symptoms in clinical trials and used less common designs like platform trials and human challenge studies [5].
In this way, scientists worldwide have been working hard to find treatments and ways to avoid getting sick. In the search for treatments to stop the spread of DENV, new technologies like RNA interference (RNAi) and CRISPR have become more popular.
2. Dengue treatment technologies
As previously stated, diverse dengue treatment technologies are currently being developed. Our text will elaborate on RNAi and CRISPR, two technologies that are getting more and more interesting in this field.
2.1 RNAi
Post-transcriptional gene silencing (PTGS) is observed in many species, including plants, fungi, and animals. RNA interference (RNAi), an ancient defense mechanism, is the common denominator [6].
When put into cells, long dsRNA can efficiently and precisely lead to the degradation of cognate mRNAs in a way that depends on the gene. This powerful technology has been used to change how genes are expressed, determine how signals are sent, and determine what genes do on a whole-genome scale [7].
Researchers worldwide have used RNA interference (RNAi) for basic research. They are currently making drugs based on RNAi to prevent and treat viral infections, tumors, and metabolic disorders in humans [8].
Although there have been significant improvements in the treatment of viral diseases, current medications and vaccines are still limited by a variety of issues, including toxicity, complexity, cost, and resistance. Eukaryotic get a defense mechanism called RNAi that helps them avoid getting infected by viruses [9].
Viral mRNA is sent to cellular enzymes to be broken down, which can stop the production of crucial viral proteins. Human cells can now be protected from viruses that cause disease thanks to new technology [10].
2.1.1 Machinery of RNAi
Through biochemical and genetic research, scientists have discovered how dsRNA causes the breakdown of target messenger RNA at the molecular level. RNA interference involves the initiation and effector steps [9].
Dicer, a member of the RNase III family of ATP-dependent ribonucleases, binds to long dsRNA (introduced directly or via a transgene or virus) with high affinity and cleaves it into small interfering RNA (siRNA) duplexes. An N-terminal DEXH-box RNA helicase domain, a domain with an unknown function (DUF283), a PAZ domain, two RIII domains, and a dsRNA-binding domain are all common features of dicer enzymes (dsRBD). In order to create siRNAs or microRNAs (miRNAs), the dicer can cut stem-loop precursors from dsRNA [11].
siRNAs are dsRNA duplexes with 21–23 nucleotides, 2-nt 3′ overhangs, a 5′-monophosphate, and a 3′-hydroxyl group. During the “effector” (RISC) step, siRNA duplexes are incorporated into the RNA-induced silencing complex (RISC). The phosphorylation of the 5′-terminus of siRNA is required for entry into RISC. A helicase domain of RISC binds to one end of the duplex and unwinds it ATP-dependently [12].
The thermodynamic stability of the initial few base pairs of siRNA can affect the proportion of RISC containing antisense or sense siRNA strands. Dicer with R2D2 (Dcr-2-associated protein) binds siRNA and assists with its loading onto RISC. The active RISC then identifies the homologous transcript via base-pairing interactions and cleaves the mRNA between the 10th and 11th nucleotides of the 5′ end of the siRNAs [13, 14].
Animals make these short RNA species using Dicer to cut long (70 nt) endogenous precursors with an imperfect hairpin RNA structure into short RNA species. Mature miRNAs stop translation by partially matching their bases to the 5′ or 3′ ends of mRNAs. A miRNA that is completely complementary to its target mRNA (endogenous siRNA) can cause the target mRNA to be broken down [15, 16].
Furthermore, it is likely that many other proteins, such as eukaryotic translation initiation factor 2C2 (eIF2C2) and Argonaute proteins, work in both pathways. Argonaute proteins are the essential RISC components. With two distinct domains, PAZ and PIWI, they are evolutionarily conserved. The PIWI domain is exclusive to Argonautes, whereas the PAZ domain is shared with proteins 21 from the Dicer family [13, 17].
2.1.2 Silencing mechanisms of RNAi
The mRNA targets multiple siRNA sequences, and long dsRNA effectively stops the gene from being expressed. Virus-infected cells always produce dsRNA, but viruses can evade a severe cellular response. The dsRNA binds to dsRNA-binding proteins (dsRBPs), which have been shown to stop RNA interference (RNAi) and block the effects of interferon (IFN). Recent research has shown that 21-nucleotide siRNAs cannot cause mammalian cells to make interferon. Since siRNAs can stop viruses from spreading, more and more scientists are becoming interested in this field [16].
It has been shown that siRNA molecules can stop a virus from spreading by sending viral mRNA to be broken down. Compared to other conventional medications, siRNA has numerous advantages. Because sequence-specific target mRNA and complementary siRNA make it much easier and more flexible to choose target sites, siRNAs can stop mRNA from doing its job by going after different parts of the target mRNA for a given mRNA molecule. Second, to silence a gene, a substoichiometric amount of siRNA is enough to reduce homologous mRNA by a lot within 24 hours [18].
Third, siRNAs can cause cognate mRNA to break down in the cells of different species. Scientists are working on siRNA delivery systems that will make it easier for siRNA to get into the cells of almost all organs. Fourthly, siRNAs appear to have no negative effect on cell control mechanisms. The length of the siRNA and how similar it is to the target region of the cognate transcription make sure that only the desired transcript will be destroyed. siRNAs lacking suitable targets appear to be inactive within cells. The best thing about RNAi as a way to fight viruses is that it is very specific and does not have any bad side effects.
Fifthly, siRNAs can effectively silence genes. Using plasmid and viral vectors, siRNAs can exhibit their long-lasting biological effects. The siRNAs made in vivo or in vitro and then put into cultured cells or animals may silence messenger RNA (mRNA) molecules based on their sequence. Since proof-of-concept studies showed that siRNAs work, they have become a popular alternative therapy [19].
2.1.3 RNAi and DENV
RNA interference is an exciting field of functional genomics that can silence viral genes. This virus-fighting system, found in many eukaryotes, could be used to treat flavivirus infections in hosts. However, RNA interference against flaviviruses has received scant research [20, 21].
RNAi has been utilized against multiple human pathogens, such as human immunodeficiency virus type 1, hepatitis C virus, hepatitis B virus, poliovirus, influenza virus A, and DENV. In the cytoplasm, the ssRNA genomes of these viruses are visible and could be used as RNAi targets. Between viral RNA uncoating and viral replication, this occurs [22].
Certain mosquitoes are capable vectors of arthropod-borne viruses (arboviruses), while others are not. It has been established that Aedes species possess a Rnai pathway. The first piece of evidence is that recombinant Sindbis viruses expressing an RNA fragment from a genetically unrelated dengue-2 virus (DENV-2) inhibit DENV-2 replication in
The second evidence is that the replication of the homologous virus is stopped when dsRNA or siRNA made from the arbovirus genome is put into C6/36 (
Both innate and adaptive immune responses highly influence the DENV infection, but little is known about the innate immune response of the mosquito vector
Dendritic cells (DC) infected with AAV-siRNA demonstrated a dose-dependent reduction in dengue infection. DCs treated with AAV-siRNA were also protected from dengue-induced apoptosis. Thus, AAV-mediated siRNA delivery can reduce dengue infection and replication in humans. Through extensive siRNA screening, more than 100 proteins of host factors involved in DENV replication have been identified. In drug design, these host factors serve as drug targets. Host factors (proteases, glucosidases, other) have yet to be identified via siRNA screening. Also, these studies could not find genes for natural immunity that protect against DENV infection. The biggest problem is getting siRNA to patients; a good way to do that has yet to be found [25].
The fact that DENV-2-derived siRNA was found in RNA extracts from the midguts of Carb77 and that the resistance phenotype was lost when the RNAi pathway was blocked [26] showed that an RNAi response caused DENV-2 resistance. C6/36 cells transfected with siRNA against the dengue PreM gene were then attacked by the DENV1 virus [25].
After seven days, the number of transfected cells that were still alive increased by 2.26 times, while the amount of virus RNA dropped by 97.54 percent. This finding provides evidence that siRNA inhibits dengue replication effectively [27]. Mukherjee et al. [28] showed that DENV can replicate in Drosophila S2 cells and that the RNAi pathway controls DENV replication. The downregulation of HSP60 in infected cells reduced viral load, RNA copy number, and IFN concentration [29].
High levels of HSP60 in infected cells make it easier for viruses to multiply and could be a target for treating dengue infection. RNAi, plasmid transfection, and inducible vectors can temporarily turn off genes’ effects. siRNA is extremely specific for target RNA. Therefore, siRNA is important for discovering and understanding gene function [29, 30].
Using siRNA to silence the attachment receptor and clathrin-mediated endocytosis, it is possible to lower the amount of virus in like this using siRNA to stop the attachment receptor and clathrin-mediated endocytosis, the amount of virus in the body can be lowered. Thus, preventing the progression of dengue fever to more severe forms (DHF/DSS) [31].
Importantly DENV infection identified key cellular genes involved in endocytosis and cytoskeletal dynamics. siRNA targeting genes involved in clathrin-mediated endocytosis prevented DENV entry into Huh7 cells [32]. Villegas-Rosales et al. [26] recently found that three siRNAs that target NS4B and NS5 sequences can silence four DENV genome serotypes.
Combining siRNA and endogenous RNAi processing machinery can prevent severe dengue infection. DC-3 siRNA is a new way to fight against different serotypes of Dengue, so it can help develop new treatment plans [33].
Korrapati et al. [34] used a human adenovirus type 5 vector that could not replicate to target conserved viral genome sites with short-hairpin RNA. This short-hairpin RNA grows into the corresponding siRNA and stops all four dengue serotypes from making antigens and more viruses.
These studies and their clear results show that RNA interference prevents DENV from replicating in cell cultures and animal models [35].
2.2 CRISPR
This adaptive immune response protects bacteria and archaea from bacteriophages and plasmids. CRISPR-Cas immunity is mediated by crRNA and an endonuclease Cas that targets genetic elements. The mode of action includes three distinct phases: acquisition, expression, and interference. In the acquisition step, foreign nucleic acids are added in a specific order as new CRISPR spacers to a CRISPR array made up of repeat sequences. This creates a memory of the genetic elements outside the cell [36, 37, 38].
The CRISPR locus is turned into a pre-CRISPR RNA transcript (pre-crRNA) during the expression step. This pre-crRNA is then changed into a mature crRNA that has some CRISPR spacer sequences joined to some CRISPR repeats. A transactivating RNA (tracrRNA) is also made by the CRISPR locus. Its repeat regions match those of the crRNA transcripts. In addition to the CRISPR array, the CRISPR locus can code for one or more Cas nucleases, such as Cas9. During the interference phase, the repeat region sequences that match each other bind to make a hybrid of crRNA and tracrRNA. This RNA hybrid tells the Cas nuclease to go after complementary DNA sequences. This allows invading genetic elements to be found and cut out [39, 40].
Most CRISPR effector proteins depend on a protospacer-adjacent motif (PAM) in the targeted nucleic acid, like NGG for Cas9. The PAM is essential for self-DNA recognition, cleavage, and differentiation from non-self DNA [41].
For Cas9, perfect complementarity will cause the endonuclease to change shape, leading to a structure that can cut DNA. The protein and RNA parts of Streptococcus pyogenes’s class 2 CRISPR system have been changed to work in eukaryotic cells, like human cells [42].
Mammalian cells send Cas9 to the nucleus by joining it to a nuclear localization signal (NLS) that works best with human codons. To make single-guide RNAs (sgRNAs) for editing the genome that looks like the natural crRNA–tracrRNA hybrid, crRNA-like sequences are fused to a partial tracrRNA using a synthetic stem-loop [43].
2.2.1 Gain-of-function approaches
Strategies that use the ectopic overexpression of genes have helped find cell surface receptors needed for viruses to get into cells and host factors that stop viruses from getting into cells. An infection-resistant cell line is often transduced with a complementary DNA library (cDNA library) made from an infection-permissive cell type to find entry receptors. In a cDNA library made from hepatocellular carcinoma cells and a non-permissive cell line, claudin 1 (CLDN1) and occludin (OCLN) were found to be HCV entry receptors [44, 45].
In addition to identifying receptors, an independent expression screen revealed that SEC14-like protein 2 (SEC14L2), a cytosolic lipid-binding protein, promotes the replication of clinical strains of HCV20. Also, proteins important for the immune system’s natural defenses against DNA and RNA viruses were found using a library of about 380 interferon-stimulated genes (ISGs) [46, 47, 48].
In addition to these screens, full cDNA libraries with all annotated ORFs from humans have been cloned into lentiviral expression vectors. This has led to the creation of an expression vector library, which will likely make the gain of function screens more useful for studying the interactions between a host and a pathogen [49, 50].
2.2.2 Function loss genetic analyses
Screens for loss of function rely on the stable knockdown or knockout of genes. Initial RNA interference-based approaches have yielded valuable insights into virus-host relationships [50].
In contrast to RNAi, which only stops some genes from being expressed, recent technological advances have made it possible to stop all genes from being expressed. One way is to use insertion mutagenesis to change genes in haploid cell lines in culture. This is called “haploid genetic screening.” Retroviral gene traps with a splice acceptor site, for example, can become part of the host genome and cause truncated mRNA transcripts to be made. Completely turning off the expression of a gene can have big effects on viral replication and help figure out which parts of the host are most important for viral infection. Using insertion mutagenesis in haploid cells, researchers have found the essential receptors for many viruses, like Ebola and Lassa [51, 52].
As receptors, both viruses utilize abundant lysosomal proteins. The interaction between the Ebola virus glycoprotein and its receptor Niemann–Pick C1 protein (NPC1) is set off by cathepsin cleavage. In contrast, the interaction between the Lassa virus glycoprotein and its receptor lysosome-associated membrane glycoprotein 1 (LAMP1) is set off by acidification of the endosome. Subsequent structural studies determined the viral glycoprotein and NPC1 binding interface. During the 2013–2016 Ebola epidemic, several mutations occurred in the host-binding site of the viral glycoprotein [53, 54, 55, 56].
These changes made the virus more infectious in cells from primates but not in cells from rodents. This implies that they aided the virus’s adaptation and spread in humans. Haplotypic genetic screens helped find a cellular phospholipase that lets viruses get around an antiviral restriction mechanism that works against many
Recently, a haploid screen found a protein-based receptor that allows multiple different serotypes of adeno-associated virus (AAV) to enter cells. This may change how AAV is used as a vector for gene therapy. Loss of function screens is a good way to find out which host factors are necessary for viral replication, as shown by these and other studies [58].
2.2.3 Insights from CRISPR-CAS screens
CRISPR-Cas screens have a great potential for identifying host factors essential for viral pathogenesis, which could lead to developing new antivirals. CRISPR-Cas screens have been used to study several viruses [59].
CRISPR-Cas screens could find host factors essential for viral pathogenesis, which could lead to developing new antivirals [60].
Using CRISPR-Cas screens, the cotranslational and posttranslational insertion of several membrane-spanning hydrophobic helices and polyprotein cleavage by a viral protease and several host proteases into the mature viral proteins have been studied. Even though these processes are known, not enough is known about the involved host proteins [61, 62].
Using DENV, different CRISPR-Cas screens have each found several ER proteins needed for the virus to spread. A lot of these proteins are needed for the endoplasmic reticulum (ER) to do its important job of making membrane and secretory proteins [63].
The identified proteins have been implicated specifically in N-linked glycosylation, ERAD, and signal peptide insertion and processing. Notably, these proteins were identified in duplicate screens conducted in the same lab as well as independent screens conducted in separate labs using distinct cell lines and virus strains. There was also substantial overlap between the results of haploid genetic testing. This technology’s remarkable reproducibility is a major advantage [64].
Furthermore, CRISPR-Cas technology is a reliable way to test candidate genes and figure out how gene knockouts affect a virus copies itself. Gene knockouts differ from knockdown methods like RNA interference (RNAi) because they are permanent and do not lead to different levels of depletion. This lets people use quantitative tests for virus replication, like quantitative PCR, immunostaining, or plaque assays, to compare genes accurately. When the most enriched host factors were taken out of the screens, flavivirus replication dropped by 100–10,000,000. This shows that pooled sgRNA screens could be used to find host factors needed for virus replication [65].
CRISPR-Cas knockout cells can also be used to understand the molecular basis of knockout phenotypes and find out which stage of a virus’s life cycle the host factor is involved. For instance, it was discovered that the OST complex is required for viral RNA synthesis but not for viral entry and translation [63].
The OST complex glycosylates newly synthesized proteins via N-linked glycosylation. In mammalian cells, there are two different OST multiprotein complexes. Each comprises a catalytic subunit (one of two paralogs, STT3A or STT3B) and accessory subunits [66].
DENV replication needs both isoforms, as either knocking out STT3A or STT3B stopped DENV replication completely. Other
SEC61A1 and SEC63, which form the translocon channel in the ER membrane; the translocon-associated protein (TRAP) complex, which stimulates cotranslational translocation of polypeptides into the ER73; and the signal peptidase complex, which cuts signal peptides in the ER lumen are also essential for flavivirus replication. Multiple
Other host factors essential for flavivirus replication include SEC61A1 and SEC63, which form the translocon channel in the ER membrane; the translocon-associated protein (TRAP) complex, which stimulates cotranslational translocation of polypeptides into the ER73; and the signal peptidase complex, which cuts signal peptides in the ER lumen. Multiple flaviviruses exhibited severe polyprotein cleavage deficiencies when a subset of signal peptidase complex subunits (SPCSs) was absent. In particular, separating the structural proteins prM and E from the polyprotein was hard for the virus particles to get out of the cell [71].
It is important to know that genetic screenings of WNV and DENV have not found a specific receptor for viruses to enter host cells. This is not the case with many other viruses, such as Ebola. This is probably because there is more than one way for a virus to get into a cell. If a virus receptor is knocked out, the cell is still open to infection in a different way. Indeed, numerous DENV receptors have been identified. Nevertheless, CRISPR-Cas screens have contributed to our understanding of flavivirus biology by revealing the central role of ER complexes in flavivirus infection promotion [51, 71].
2.2.4 CRISPR-CAS antiviral strategies
The CRISPR-Cas technology could be used to prevent and treat diseases by going after viruses and the things that spread them. Vector control has been used to stop the spread of viruses carried by vectors, like ZIKV, DENV, and yellow fever [72].
Using CRISPR-Cas tools, scientists have made gene drives that could reduce the number of mosquitoes. CRISPR-Cas technology could also be used to treat HIV, HBV, HCV, and the herpes simplex virus, which do not go away on their own. HBV covalently closed circular DNA (cccDNA), a sign of a persistent HBV infection, has been successfully targeted in cell cultures and animal models [73, 74, 75].
Additionally, CRISPR-Cas screens can be utilized to determine the mechanism of action of antivirals. For example, CRISPR-Cas and short hairpin RNA (shRNA) screens were used to determine how the antiviral drug GSK983 works. This drug may stop a wide range of RNA and DNA viruses. By stopping the enzyme dihydroorotate dehydrogenase from making pyrimidine in cells and lowering the number of nucleotides inside cells, which are needed for viral nucleic acid synthesis, GSK983 was found to stop viruses from spreading [76, 77].
3. Conclusions
Technologies like CRISPR and RNAi have become important ways to learn more about how viruses, like DENV, cause infections.
In addition, it is noteworthy that both CRISPR and RNAi have emerged as viable alternatives for treating viral infections and managing
The new information we get from these technologies will be significant for a better understanding of how viruses replicate and interact with their hosts.
References
- 1.
Mukhtar M, Wajeeha AW, Zaidi N, Bibi N. Engineering modified mRNA-based vaccine against dengue virus using computational and reverse vaccinology approaches. IJMS. 2022; 23 (22):13911 - 2.
Rao MRK, Padhy RN, Das MK. Episodes of the epidemiological factors correlated with prevailing viral infections with dengue virus and molecular characterization of serotype-specific dengue virus circulation in eastern India. Infection, Genetics and Evolution. 2018; 58 :40-49 - 3.
Horstick O, Tozan Y, Wilder-Smith A. Reviewing Dengue: Still a neglected tropical disease? PLoS Neglected Tropical Diseases. 2015; 9 (4):e0003632 - 4.
Chen H-R, Lai Y-C, Yeh T-M. Dengue virus non-structural protein 1: A pathogenic factor, therapeutic target, and vaccine candidate. Journal of Biomedical Science. 2018; 25 (1):58 - 5.
Lin RJ, Lee TH, Leo YS. Dengue in the elderly: A review. Expert Review of Anti-Infective Therapy. 2017; 15 (8):729-735 - 6.
Kakumani PK, Ponia SS, Sood V, Chinnappan M, Banerjea AC, et al. Role of RNA interference (RNAi) in dengue virus replication and identification of NS4B as an RNAi suppressor. Journal of Virology. 2013; 87 (16):8870-8883 - 7.
Saify Nabiabad H, Amini M, Demirdas S. Specific RNAi delivery using Spike’s aptamer-functionalized lipid nanoparticles for targeting SARS-CoV-2: A strong anti-Covid drug in a clinical case study. Chemical Biology & Drug Design. 2022; 99 (2):233-246 - 8.
Berkhout B. RNAi-mediated antiviral immunity in mammals. Current Opinion in Virology. 2018; 32 :9-14 - 9.
Olson KE, Blair CD. Arbovirus-mosquito interactions: RNAi pathway. Current Opinion in Virology. 2015; 15 :119-126 - 10.
Uludağ H, Parent K, Aliabadi HM, Haddadi A. Prospects for RNAi Therapy of COVID-19. Frontiers in Bioengineering and Biotechnology. 2020; 8 :916 - 11.
Aliabadi HM, Bahadur KCR, Bousoik E, Hall R, Barbarino A, Thapa B, et al. A systematic comparison of lipopolymers for siRNA delivery to multiple breast cancer cell lines: In vitro studies. Acta Biomaterialia. 2020; 102 :351-366 - 12.
Mysara M, Garibaldi JM, Elhefnawi M. MysiRNA-designer: A workflow for efficient siRNA design. PLoS One. 2011; 6 (10):e25642 - 13.
Casseb SMM, Khayat AS, de Souza JES, de Oliveira EHC, Dos Santos SEB, da Costa Vasconcelos PF, et al. Anticipating the next chess move: Blocking SARS-CoV-2 replication and simultaneously disarming viral escape mechanisms. Genes (Basel). 2022; 13 (11):1-14 - 14.
Sartaj Sohrab S, Aly El-Kafrawy S, Ibraheem AE. In silico prediction and experimental evaluation of potential siRNAs against SARS-CoV-2 inhibition in Vero E6 cells. Journal of King Saudi University Science. 2022; 34 (4):102049 - 15.
Baldassi D, Ambike S, Feuerherd M, Cheng C-C, Peeler DJ, Feldmann DP, et al. Inhibition of SARS-CoV-2 replication in the lung with siRNA/VIPER polyplexes. Journal of Controlled Release. 2022; 345 :661-674 - 16.
Dana H, Chalbatani GM, Mahmoodzadeh H, Karimloo R, Rezaiean O, Moradzadeh A, et al. Molecular Mechanisms and Biological Functions of siRNA. International Journal of Biomedical Sciences. 2017; 13 (2):48-57 - 17.
Ambike S, Cheng C-C, Feuerherd M, Velkov S, Baldassi D, Afridi SQ , et al. Targeting genomic SARS-CoV-2 RNA with siRNAs allows efficient inhibition of viral replication and spread. Nucleic Acids Research. 2022; 50 (1):333-349 - 18.
Ryu YC, Kim KA, Kim BC, Wang H-MD, Hwang BH. Novel fusion peptide-mediated siRNA delivery using self-assembled nanocomplex. Journal of Nanobiotechnology. 2021; 19 (1):44 - 19.
Hu B, Zhong L, Weng Y, Peng L, Huang Y, Zhao Y, et al. Therapeutic siRNA: State of the art. Signal Transduction and Targeted Therapy. 2020; 5 (1):101 - 20.
Wu X, Hong H, Yue J, Wu Y, Li X, Jiang L, et al. Inhibitory effect of small interfering RNA on dengue virus replication in mosquito cells. Virology Journal. 2010; 7 :270 - 21.
Yang J, Zou L, Yang Y, Yuan J, Hu Z, Liu H, et al. Superficial vimentin mediates DENV-2 infection of vascular endothelial cells. Scientific Reports. 2016; 6 :38372 - 22.
Ketzinel-Gilad M, Shaul Y, Galun E. RNA interference for antiviral therapy. The Journal of Gene Medicine. 2006; 8 (8):933-950 - 23.
Thompson R, Martin Del Campo J, Constenla D. A review of the economic evidence of Aedes-borne arboviruses and Aedes-borne arboviral disease prevention and control strategies. Expert Review of Vaccines. 2020; 19 (2):143-162 - 24.
Sánchez-Vargas I, Scott JC, Poole-Smith BK, Franz AWE, Barbosa-Solomieu V, Wilusz J, et al. Dengue virus type 2 infections of Aedes aegypti are modulated by the mosquito’s RNA interference pathway. PLoS Pathogens. 2009; 5 (2):e1000299 - 25.
Yue J, Wu X, Wu Y, Li X, Jiang L, Li Q , et al. Study on the inhibitory effect of RNA interference on replication of dengue virus. Bing Du Xue Bao. 2010; 26 (5):373-378 - 26.
Villegas-Rosales PM, Méndez-Tenorio A, Ortega-Soto E, Barrón BL. Bioinformatics prediction of siRNAs as potential antiviral agents against dengue viruses. Bioinformation. 2012; 8 (11):519-522 - 27.
Franz AWE, Sanchez-Vargas I, Adelman ZN, Blair CD, Beaty BJ, James AA, et al. Engineering RNA interference-based resistance to dengue virus type 2 in genetically modified Aedes aegypti. Proceedings of the National Academy Science USA. 2006; 103 (11):4198-4203 - 28.
Mukherjee S, Hanley KA. RNA interference modulates replication of dengue virus in Drosophila melanogaster cells. BMC Microbiology. 2010; 10 :127 - 29.
Padwad YS, Mishra KP, Jain M, Chanda S, Karan D, Ganju L. RNA interference mediated silencing of Hsp60 gene in human monocytic myeloma cell line U937 revealed decreased dengue virus multiplication. Immunobiology. 2009; 214 (6):422-429 - 30.
Ashfaq UA, Yousaf MZ, Aslam M, Ejaz R, Jahan S, Ullah O. siRNAs: Potential therapeutic agents against hepatitis C virus. Virology Journal. 2011; 8 :276 - 31.
Alhoot MA, Wang SM, Sekaran SD. RNA interference mediated inhibition of dengue virus multiplication and entry in HepG2 cells. PLoS One. 2012; 7 (3):e34060 - 32.
Ang F, Wong APY, Ng MM-L, Chu JJH. Small interference RNA profiling reveals the essential role of human membrane trafficking genes in mediating the infectious entry of dengue virus. Virology Journal. 2010; 7 :24 - 33.
Stein DA, Perry ST, Buck MD, Oehmen CS, Fischer MA, Poore E, et al. Inhibition of dengue virus infections in cell cultures and in AG129 mice by a small interfering RNA targeting a highly conserved sequence. Journal of Virology. 2011; 85 (19):10154-10166 - 34.
Korrapati AB, Swaminathan G, Singh A, Khanna N, Swaminathan S. Adenovirus delivered short hairpin RNA targeting a conserved site in the 5’ non-translated region inhibits all four serotypes of dengue viruses. PLoS Neglected Tropical Diseases. 2012; 6 (7):e1735 - 35.
van Rij RP, Andino R. The silent treatment: RNAi as a defense against virus infection in mammals. Trends in Biotechnology. 2006; 24 (4):186-193 - 36.
Brenner S. The genetics of Caenorhabditis elegans. Genetics. 1974; 77 (1):71-94 - 37.
Hartwell LH, Culotti J, Reid B. Genetic control of the cell-division cycle in yeast. I. Detection of mutants. Proceedings of the National Academy Science USA. 1970; 66 (2):352-359 - 38.
Rutschmann S, Jung AC, Zhou R, Silverman N, Hoffmann JA, Ferrandon D. Role of Drosophila IKK gamma in a toll-independent antibacterial immune response. Nature Immunology. 2000; 1 (4):342-347 - 39.
Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, et al. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013; 339 (6121):819-823 - 40.
Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, et al. RNA-guided human genome engineering via Cas9. Science. 2013; 339 (6121):823-826 - 41.
Li B, Clohisey SM, Chia BS, Wang B, Cui A, Eisenhaure T, et al. Genome-wide CRISPR screen identifies host dependency factors for influenza A virus infection. Nature Communications. 2020; 11 (1):164 - 42.
Evers B, Jastrzebski K, Heijmans JPM, Grernrum W, Beijersbergen RL, Bernards R. CRISPR knockout screening outperforms shRNA and CRISPRi in identifying essential genes. Nature Biotechnology. 2016; 34 (6):631-633 - 43.
Lin H, Li G, Peng X, Deng A, Ye L, Shi L, et al. The use of crispr/cas9 as a tool to study human infectious viruses. Frontiers in Cellular and Infection Microbiology. 2021; 11 :590989 - 44.
Evans MJ, von Hahn T, Tscherne DM, Syder AJ, Panis M, Wölk B, et al. Claudin-1 is a hepatitis C virus co-receptor required for a late step in entry. Nature. 2007; 446 (7137):801-805 - 45.
Ploss A, Evans MJ, Gaysinskaya VA, Panis M, You H, de Jong YP, et al. Human occludin is a hepatitis C virus entry factor required for infection of mouse cells. Nature. 2009; 457 (7231):882-886 - 46.
Saeed M, Andreo U, Chung H-Y, Espiritu C, Branch AD, Silva JM, et al. SEC14L2 enables pan-genotype HCV replication in cell culture. Nature. 2015; 524 (7566):471-475 - 47.
Schoggins JW, MacDuff DA, Imanaka N, Gainey MD, Shrestha B, Eitson JL, et al. Pan-viral specificity of IFN-induced genes reveals new roles for cGAS in innate immunity. Nature. 2014; 505 (7485):691-695 - 48.
Schoggins JW, Wilson SJ, Panis M, Murphy MY, Jones CT, Bieniasz P, et al. A diverse range of gene products are effectors of the type I interferon antiviral response. Nature. 2011; 472 (7344):481-485 - 49.
Tang N, Zhang Y, Shen Z, Yao Y, Nair V. Application of CRISPR-Cas9 Editing for Virus Engineering and the Development of Recombinant Viral Vaccines. The CRISPR Journal. 2021; 4 (4):477-490 - 50.
Ramage H, Cherry S. Virus-Host Interactions: From Unbiased Genetic Screens to Function. Annual Review of Virology. 2015; 2 (1):497-524 - 51.
Carette JE, Raaben M, Wong AC, Herbert AS, Obernosterer G, Mulherkar N, et al. Ebola virus entry requires the cholesterol transporter Niemann-Pick C1. Nature. 2011; 477 (7364):340-343 - 52.
Jae LT, Raaben M, Herbert AS, Kuehne AI, Wirchnianski AS, Soh TK, et al. Virus entry. Lassa virus entry requires a trigger-induced receptor switch. Science. 2014; 344 (6191):1506-1510 - 53.
Miller EH, Obernosterer G, Raaben M, Herbert AS, Deffieu MS, Krishnan A, et al. Ebola virus entry requires the host-programmed recognition of an intracellular receptor. The EMBO Journal. 2012; 31 (8):1947-1960 - 54.
Côté M, Misasi J, Ren T, Bruchez A, Lee K, Filone CM, et al. Small molecule inhibitors reveal Niemann-Pick C1 is essential for Ebola virus infection. Nature. 2011; 477 (7364):344-348 - 55.
Bornholdt ZA, Ndungo E, Fusco ML, Bale S, Flyak AI, Crowe JE, et al. Host-Primed Ebola Virus GP Exposes a Hydrophobic NPC1 Receptor-Binding Pocket, Revealing a Target for Broadly Neutralizing Antibodies. MBio. 2016; 7 (1):1-11 - 56.
Wang H, Shi Y, Song J, Qi J, Lu G, Yan J, et al. Ebola viral glycoprotein bound to its endosomal receptor Niemann-Pick C1. Cell. 2016; 164 (1-2):258-268 - 57.
Staring J, von Castelmur E, Blomen VA, van den Hengel LG, Brockmann M, Baggen J, et al. PLA2G16 represents a switch between entry and clearance of Picornaviridae. Nature. 2017; 541 (7637):412-416 - 58.
Pillay S, Meyer NL, Puschnik AS, Davulcu O, Diep J, Ishikawa Y, et al. An essential receptor for adeno-associated virus infection. Nature. 2016; 530 (7588):108-112 - 59.
Puschnik AS, Majzoub K, Ooi YS, Carette JE. A CRISPR toolbox to study virus-host interactions. Nature Reviews. Microbiology. 2017; 15 (6):351-364 - 60.
Zhang Y, Li M. Genome editing technologies as cellular defense against viral pathogens. Frontiers in Cell and Development Biology. 2021; 9 :716344 - 61.
Bhatt S, Gething PW, Brady OJ, Messina JP, Farlow AW, Moyes CL, et al. The global distribution and burden of Dengue. Nature. 2013; 496 (7446):504-507 - 62.
Kraemer MUG, Sinka ME, Duda KA, Mylne AQN, Shearer FM, Barker CM, et al. The global distribution of the arbovirus vectors Aedes aegypti and Ae. albopictus. eLife. 2015; 4 :e08347 - 63.
Marceau CD, Puschnik AS, Majzoub K, Ooi YS, Brewer SM, Fuchs G, et al. Genetic dissection of Flaviviridae host factors through genome-scale CRISPR screens. Nature. 2016; 535 (7610):159-163 - 64.
Cherepanova NA, Gilmore R. Mammalian cells lacking either the cotranslational or posttranslocational oligosaccharyltransferase complex display substrate-dependent defects in asparagine linked glycosylation. Scientific Reports. 2016; 6 :20946 - 65.
Olzmann JA, Kopito RR, Christianson JC. The mammalian endoplasmic reticulum-associated degradation system. Cold Springer Harbor Perspective Biology. 2013; 5 (9):1-16 - 66.
Lino CA, Harper JC, Carney JP, Timlin JA. Delivering CRISPR: A review of the challenges and approaches. Drug Delivery. 2018; 25 (1):1234-1257 - 67.
Lin DL, Cherepanova NA, Bozzacco L, MacDonald MR, Gilmore R, Tai AW. Dengue virus hijacks a noncanonical oxidoreductase function of a cellular oligosaccharyltransferase complex. MBio. 2017; 8 (4):1-16 - 68.
Kulkarni MA, Duguay C, Ost K. Charting the evidence for climate change impacts on the global spread of malaria and Dengue and adaptive responses: A scoping review of reviews. Globalization and Health. 2022; 18 (1):1 - 69.
Kalinina NO, Khromov A, Love AJ, Taliansky ME. CRISPR applications in plant virology: Virus resistance and beyond. Phytopathology. 2020; 110 (1):18-28 - 70.
Adli M. The CRISPR tool kit for genome editing and beyond. Nature Communications. 2018; 9 (1):1911 - 71.
Zhang R, Miner JJ, Gorman MJ, Rausch K, Ramage H, White JP, et al. A CRISPR screen defines a signal peptide processing pathway required by flaviviruses. Nature. 2016; 535 (7610):164-168 - 72.
Harris AF, Nimmo D, McKemey AR, Kelly N, Scaife S, Donnelly CA, et al. Field performance of engineered male mosquitoes. Nature Biotechnology. 2011; 29 (11):1034-1037 - 73.
Zhen S, Hua L, Liu YH, Gao LC, Fu J, Wan DY, et al. Harnessing the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated Cas9 system to disrupt the hepatitis B virus. Gene Therapy. 2015; 22 (5):404-412 - 74.
Kennedy EM, Bassit LC, Mueller H, Kornepati AVR, Bogerd HP, Nie T, et al. Suppression of hepatitis B virus DNA accumulation in chronically infected cells using a bacterial CRISPR/Cas RNA-guided DNA endonuclease. Virology. 2015; 476 :196-205 - 75.
Ramanan V, Shlomai A, Cox DBT, Schwartz RE, Michailidis E, Bhatta A, et al. CRISPR/Cas9 cleavage of viral DNA efficiently suppresses hepatitis B virus. Scientific Reports. 2015; 5 :10833 - 76.
Deans RM, Morgens DW, Ökesli A, Pillay S, Horlbeck MA, Kampmann M, et al. Parallel shRNA and CRISPR-Cas9 screens enable antiviral drug target identification. Nature Chemical Biology. 2016; 12 (5):361-366 - 77.
Harvey R, Brown K, Zhang Q , Gartland M, Walton L, Talarico C, et al. GSK983: A novel compound with broad-spectrum antiviral activity. Antiviral Research. 2009; 82 (1):1-11